Suresh Niraj, Stephens Sean A, Adams Lexor, Beck Anthon N, McKinney Adriana L, Varga Tamas
Environmental Molecular Sciences Laboratory.
Environmental Molecular Sciences Laboratory;
J Vis Exp. 2016 Apr 26(110):53788. doi: 10.3791/53788.
Plant roots play a critical role in plant-soil-microbe interactions that occur in the rhizosphere, as well as processes with important implications to climate change and crop management. Quantitative size information on roots in their native environment is invaluable for studying root growth and environmental processes involving plants. X-ray computed tomography (XCT) has been demonstrated to be an effective tool for in situ root scanning and analysis. We aimed to develop a costless and efficient tool that approximates the surface and volume of the root regardless of its shape from three-dimensional (3D) tomography data. The root structure of a Prairie dropseed (Sporobolus heterolepis) specimen was imaged using XCT. The root was reconstructed, and the primary root structure was extracted from the data using a combination of licensed and open-source software. An isosurface polygonal mesh was then created for ease of analysis. We have developed the standalone application imeshJ, generated in MATLAB(1), to calculate root volume and surface area from the mesh. The outputs of imeshJ are surface area (in mm(2)) and the volume (in mm(3)). The process, utilizing a unique combination of tools from imaging to quantitative root analysis, is described. A combination of XCT and open-source software proved to be a powerful combination to noninvasively image plant root samples, segment root data, and extract quantitative information from the 3D data. This methodology of processing 3D data should be applicable to other material/sample systems where there is connectivity between components of similar X-ray attenuation and difficulties arise with segmentation.
植物根系在根际发生的植物 - 土壤 - 微生物相互作用中起着关键作用，同时也在对气候变化和作物管理具有重要影响的过程中发挥作用。关于根系在其原生环境中的定量尺寸信息对于研究根系生长以及涉及植物的环境过程非常宝贵。X射线计算机断层扫描（XCT）已被证明是一种用于原位根系扫描和分析的有效工具。我们旨在开发一种低成本且高效的工具，该工具能够从三维（3D）断层扫描数据中近似根系的表面积和体积，而无需考虑其形状。使用XCT对一株异穗苔草（Sporobolus heterolepis）标本的根系结构进行成像。对根系进行重建，并使用许可软件和开源软件相结合的方式从数据中提取主根结构。然后创建一个等值面多边形网格以便于分析。我们已经在MATLAB(1)中开发了独立应用程序imeshJ，用于从网格计算根系体积和表面积。imeshJ的输出结果是表面积（单位为mm²）和体积（单位为mm³）。本文描述了从成像到根系定量分析的独特工具组合的过程。XCT和开源软件的组合被证明是一种强大的组合，可用于对植物根系样本进行非侵入性成像、分割根系数据以及从3D数据中提取定量信息。这种处理3D数据的方法应该适用于其他材料/样本系统，这些系统中各组成部分具有相似的X射线衰减且在分割时存在困难。
